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| Status |
Public on May 20, 2016 |
| Title |
DDX3X regulation of global translation is impaired by medulloblastoma-associated mutations [RiboSeq] |
| Organism |
Homo sapiens |
| Experiment type |
Other
Expression profiling by high throughput sequencing
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| Summary |
Whole-genome sequencing recently identified recurrent missense mutations in the RNA helicase DDX3X in pediatric medulloblastoma (MB) and other tumors. The normal function of DDX3X is poorly understood, and the consequences of its cancer-associated mutations have not been explored. Here we used genomic, biochemical, cell biological, and animal modeling approaches to investigate normal DDX3X function and the impact of cancer-associated DDX3X mutations. Cross-linking immunoprecipitation–high-throughput sequencing (CLIPseq) analyses revealed that DDX3X binds primarily to ~1000 mature mRNA targets at binding sites spanning the full mRNA length; their enrichment in the coding regions suggests that DDX3X plays a role in translational elongation. The association of wild-type DDX3X with polysomes is consistent with this observation. Cancer-associated mutations result in loss of DDX3X from polysomes and accumulation of mutant DDX3X in stress granules (cytoplasmic accumulations of translationally arrested mRNAs). Mutation-dependent redistribution of DDX3X to stress granules is also observed in a Drosophila model system and in MB tumor cells from patients carrying DDX3X mutations. Importantly, mRNAs targeted by DDX3X are enriched in translation factors, suggesting that DDX3X regulates translation both directly and indirectly. Indeed, depletion of DDX3X by RNAi or over-expression of mutant DDX3X significantly impairs global protein synthesis. Ribosome profiling confirmed this observation and showed a 5’ bias in ribosomal occupancy, further confirming the role of DDX3X in translational elongation. Together, our data show that DDX3X is a key regulator of translation and that this function is impaired by cancer-associated mutations. Finally, we found that medulloblastoma-related mutant DDX3X can efficiently bind the wild-type form suggesting that mutant DDX3X could exert a dominant negative effect in vivo.
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| Overall design |
Examination of translation at whole genome scale under conditions of overexpression of WT DDX3X or cancer-associated DDX3X mutant G325E
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| Contributor(s) |
Valentin-Vega YA, Wang YD, Parker M, Rusch M, Smeeth D, Finkelstein D, Patmore D, Kim NC, Kanagaraj A, Moore J, Winborn B, Zhang J, Gilbertson RJ, Taylor JP |
| Citation(s) |
27180681 |
| Submission date |
Jul 03, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Yong-Dong Wang |
| E-mail(s) |
michael.wang@stjude.org
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| Phone |
9015954224
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| Organization name |
St. Jude Children's Research Hospital
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| Street address |
262 Danny Thomas Pl, MS1135
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| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38134 |
| Country |
USA |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (3) |
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| This SubSeries is part of SuperSeries: |
| GSE59096 |
DDX3X regulation of global translation is impaired by medulloblastoma-associated mutations |
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| Relations |
| BioProject |
PRJNA254361 |
| SRA |
SRP044064 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE59095_RAW.tar |
3.5 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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